In a World We Must Defend
by Glock3bb
Summary: Beneath the village of Konoha lies an ancient secret. Uncovered one day by three Genin, they must come to terms with their new destinies and the power that's inside.
1. Discovery Part I

**I wish I owned Pokémon and/or Naruto. World Domination would be mine!**

XXX

"Raaaaaah, where is he?" A twelve year old Naruto sat slumped in his chair, loudly moaning his complaint. His head rested on the classroom desk in front of him. In the same room were Sasuke and Sakura, both thinking along similar lines. It had been over an hour since the other jounin sensei had picked up their teams, but theirs still had yet to show. Even Iruka-sensei had left due to there being a curriculum meeting that afternoon. Supposedly, it was set for a time after all the gennin should have left. Naruto's patience finally reached its breaking point, so he got up and headed for the door.

"What are you doing, Naruto? We're supposed to wait here until our sensei comes for us." Naruto stopped and turned towards Sakura.

"Oh, come on." He pleaded, "This is stupid. We've been waiting for forever, and I want to do something fun."

"You can't just leave, especially not for one of your stupid pranks."

"I can, and I am. Now, you two can either come with me or stay here and keep being bored out of your mind." With that, Naruto opened the classroom door and walked out. Seconds passed in silence until Sasuke too left his chair and the room. Sakura stayed in her seat, unmoving for a moment, while a debate raged in her mind. Finally, she followed the two boys' example, not wanting to be left out.

XXX

"Get back here!" Naruto laughed as he sped away from the shinobi hot on his tail. Following just behind him were Sasuke and Sakura. They had almost finished booby trapping one of the western guard posts with itching powder when one of the packets detonated prematurely, alerting the chunin within to what the three were up too.

The chase continued until both parties reached the ring of forest surrounding the village, just inside the protective walls. Naruto saw his chance when they entered a particularly dense knot of trees, causing their pursuers to lose sight of them temporarily. He toke advantage of this by quickly creating three Kage Bushin and transforming two to look like Sasuke and Sakura. His teammates saw what his plan was and took cover within a group of nearby bushes. The clones took off, leading the unsuspecting chunin back towards the village.

Once the forest had grown quiet, the originals came out of hiding, catching their breath.

"See Sakura, we make a great team already." Her response was a sharp blow to his head.

"You idiot, what's great about almost getting caught?" Naruto cradled his injured cranium, a large bump already forming.

"You triggered the powder too early on purpose." The two turned towards Sasuke. That had been the first sentence he had spoken all afternoon. The orange clad ninja nodded, even though it was more of a statement than a question.

"Yeah, 'course I did. The chase is the best part of a prank. What's the point of doing one if no one even knows it was you?" Naruto and Sasuke looked at each other, and an unsaid conversation seemed to pass between the two. That fleeting moment ended almost instantly, and Naruto smirked. "Was the little run to much for you?" The Uchiha glared at him but didn't say anything, instead grunting and deciding to recline against one of the many trees nearby. Sakura felt out of place, not understanding what had just happened, and unsure of what to say or do. She made up her mind and turned to head back into town. Hopefully their sensei was finally at the Academy by now.

"I wouldn't do that if I were you." Naruto said when she started to leave. "Those guys will still be looking for us for awhile. They don't know when to call it quits." An idea popped into his head and he sauntered up to her. "So, Sakura, since we have some time to kill, you wanna-Gaaahh!" He had reached out an arm, wanting to place it on the trunk she was standing near, in an attempt to try to look cool. He did not count on his arm passing straight through, the rest of his body tumbling in after it. Sasuke's and Sakura's heads whipped around to where Naruto had suddenly vanished.

Their bodies tensed, not understanding quite what had happened, each trying to keep their senses alert in case they were under attack. Moments went by, and there were no signs of immediate danger. Slowly, Sasuke headed for the tree as Sakura started to examine it.

"I've never read about anything like this. It looks to be a sort of localized genjutsu that only affects this one tree." She said, puzzling over the strange phenomenon. "But why would there be a genjutsu on a tree trunk,"

"And where is the person casting it?" Sasuke finished for her. They continued their observations when Naruto's disembodied head suddenly appeared right in front of Sakura's face.

"Boo." She screamed and fell back onto her butt. Naruto's head began to laugh uproariously. "Ha ha ha ha ha ha ha ha, you should see the look on your face Sakura." The rest of the blond's body appeared as he stumbled out of the tree, holding his sides because he was guffawing so hard. He eventually composed himself and motioned for the two to follow him. "Come on, don't you guys want to see what's in here?" Naruto once more disappeared into the trunk. After a few moments of silence, Sakura was the first to follow after getting up off the ground with Sasuke right behind her.

The two found themselves in the somewhat cramped interior upon entering the tree. Looking around, they saw nothing that out of the ordinary.

"What are we supposed to be looking at, loser?" Sasuke questioned. While the genjutsu had been peculiar, nothing so far had seemed to be worth such an investment. That was when a short blink of red light caught his attention. Sakura saw it as well, and both of them squeezed closer to get a better look. The flash had come from a medium-sized button at about chest height on an adult.

"What do you think this does?" Sakura wondered out loud. The boys shrugged, not knowing themselves. "Naruto, press it." Said genin reeled back.

"What, why should I be the one to press it?" She smirked at him.

"Because you're the one that found this place, so you should get the honors."

"No way, you press it yourself!" He demanded.

"Are you kidding me? I'm not going to press a random button we found hidden in a tree. Come on Naruto, be a man." Sakura tried to goad him.

"Ladies first." He countered. Their back and forth bickering continued, neither willing to let the other have the last word. Finally, being fed up with his teammates attitudes, Sasuke pushed past them and slammed his palm against the button.

The moment he did, the wooden floor they were standing on began to drop, carrying them down below ground at a frightening speed. After a few seconds, all three were knocked from their feet by the platform's sudden deceleration. They groggily rose; the unexpected fall had taken its toll on them.

Naruto, Sasuke, and Sakura looked around the space. After the decent, they were still in the same small area, except now their only source of light was the flash from the button every few seconds.

"Well, this sucks." Naruto said. "We just found a hidden whole in the ground with nothing in it." He lazily kicked at one of the sides to prove a point, expecting to hit wood or dirt. Instead, a metallic clang rang out. His curiosity was peaked once again, and he squatted down were his foot had connected. The next instance of red light brought a surprise.

"Hey, guys, I think there's a door here." He placed his hands on the metal and moved them around, trying to find a way to open it. "Damn it, where is the handle?" The other two quickly joined his search. Again, the only light source brought an answer.

"They're sliding doors." Sasuke stated, seeing the the straight line dividing the curved wall into two parts. Setting his feet, he wiggled his fingers in to the crease and pulled with all his might. His side of the door gave way slightly. Gritting his teeth, Sasuke grunted out, "Grab the other side." Naruto paused for a moment. Sasuke had actually just asked him for help. He decided that gloating could wait until later and grabbed the other door.

A rusty screech and the grinding of gears was heard. Together, the two boys slowly pried the doors apart. Dust showered down, dislodged from its resting place high above by the movement. They finally came to a groaning halt, unable to open any further, and the sounds were swiftly engulfed by the darkness surrounding the genin. Seconds passed while Naruto and Sasuke regained their breath.

Their forced entry must have triggered something, for lights began to slowly flicker to life, one by one, bathing the area in a soft glow. It was not much, barely enough to see what was in front of them, but anything was better than the blackness to them. Before the children was a large, spacious cavern. Metal panels covered the walls and rounded ceiling. The floor was made of dirt, and had strange, white lines outlining a section of it. A muted whirling reached their ears, like the sound of machines turning on.

Naruto entered the room first, followed closely by Sasuke and Sakura. They gazed around in wonder. None of them had ever heard of such a place existing below the village. As they commenced their exploration, Naruto felt the hair on the back of his neck prickle. Something in the back of his mind told him to get out of there, but he shook his head and forcefully pushed the feeling away.

The three soon found three other doors like the one they had just come from. The one on the left side led to what seemed to be a living area. Inside were a good number of beds, two bathrooms and a kitchen. The right side room only had an odd looking machine with a glass dome inside. Other than that, it was empty, so they left and approached the final doorway, directly across from the lift.

"_Leave this place."_

A menacing voice resonated within Naruto mind right as the three were about to pass through the opening, and they froze. He turned towards the other, his hands twitching nervously.

"Please tell me you guys heard that too." Sasuke and Sakura nodded, the blonde letting out a shaky sigh of relief. From their faces, Naruto could tell they were just as nervous as he was.

"M-maybe we should go back." Sakura stuttered. Naruto saw a chance to play the hero and put on his brave face.

"No way. We're going to be doing stuff like this all the time now that we're ninja. I don't care what that stupid voice in our heads tells us; I'm going through." He grinned at the pinkette, and she felt her fears abate slightly. They formed an even tighter group and began walking forward again. The three approached the last door, and Naruto felt the feeling from before return, commanding him to turn back. His resolve was only steeled by this. It was obvious there was something hidden in here, and Naruto was determined to find out what it was. Besides, Sasuke and Sakura were not, so neither would he.

The final room was the weirdest of them all. The front and back walls were lined with bizarre devices, covered in pulsing lights, and emitting random beeps and chirps. On each side were multiple shelves, lined with hundreds of red and white balls that were about the size of a person's palm. The strangest part, though, was the creature near the back of the room.

Contained inside of a tall, glass tube, it sat suspended in a reddish-orange liquid. Wires fed from the top and bottom of the vessel were attached all along its body. Its color was difficult to discern because of the low light and fluid, but the creature's stomach and tail were definitely of a darker hue than the rest of its body. Three fingered hands ended long, lanky arms crossed over its chest. Powerful, bulging legs were tucked up close to the body. The thing's head had a vaguely feline shape to it. Its eyelids were down, and the face had a peaceful look on it, as if it were in a deep sleep.

Sakura let out a gasp at the sight of it, and all three stood staring in amazement. None of them had ever heard of such a monster. They realized at the same moment that what had started as a simple exploration of a mysterious tree was now far over their heads. They had to get out now and tell someone about this.

Before any of them could even twitch, the creature's eyes snapped open, a brilliant blue flame burning within. A piercing feeling seemed to lance directly into their brains, and the group fell to their knees, clutching their skulls in pain. Naruto could not remember anything hurting this badly. It was like something was trying to tear his head open from the inside. He could not move; his body refused to respond to any of his desperate orders. Every second became an eternity, until all three of them reached their breaking points.

"STOP IT!" They cried out, a deep power resonating in each voice. The fire in the creature's eyes died, the torment ending along with it. It blinked in confusion as it stared at the genin from within its clear prison.

The pain had gone, only to be replaced by a horrible exhaustion. Naruto's body felt weak, his limbs like lead. He fell forward onto his hands and threw up onto the floor. Naruto hazily heard the retching sounds of Sasuke and Sakura following suit. He could feel what little energy he had left rapidly dwindling away.

"_Quickly, chose one of these and press the middle button."_ It was the same voice before, ringing in the blond's mind. Three of the orbs from the right side wall floated down and settled in triangle in front of him. _"Do it now!" _The voice ordered. Acting on instinct, Naruto slowly reached out, his arm drawn to the one farthest from him. His hand cupped it, and he did as he was told. With a distinct pop, the sphere split apart. The final thing Naruto saw as he fell into unconsciousness was a white shape springing forth.

XXX

Warm. That was the first thought of Sasuke Uchiha as he started to come to. On his right side he could feel a cozy warmth radiating onto his torso. His whole body felt relaxed for the first time years; he had not rested this comfortably since the night before the massacre five years ago. Reluctantly, Sasuke forced his eyes to open. The first thing he saw was the monster from earlier floating cross-legged in the air, a blue aura enveloping its body.

In panic, the Uchiha leaped out of the bed he had been lying in and threw a handful of shuriken at the creature. He noticed that as soon as he did this, the warmth he had been feeling was gone, but he put that aside for now. Sasuke was shocked when instead of hitting the creature, the shuriken simply stopped in mid air, inches from its face, then fell to the ground.

"_Calm yourself. I mean the three of you no harm." _ Realization jolted Sasuke's mind in response to the voice in his head. This thing was what had been communicating with them before. At the mention of three, he glanced to his left and glimpsed the rough outlines of Sakura and Naruto lying on beds of their own. Sasuke quickly refocused back towards the monster. He had no reason to trust that it would keep its word.

Minutes passed. Neither one moved a muscle, letting silence reign in the room. Movement in the corner of Sasuke's eye caught his attention; it was not one of his teammates. On his bed was an odd, orange colored lizard with a fire burning on its tail. If that last fact bothered it at all, the reptile did not show it. It only stretched out and then curled up into a tighter ball. This would normally have caused Sasuke to be even more on guard, but his gut was telling him it was no threat. Besides, he had bigger problems at the moment. Namely a giant humanoid cat which could hover and stop Sasuke's weapons without opening its eyes.

A feminine shriek alerted the raven-haired boy to Sakura's awakening, and it seemed she too had an unwelcome guest in her bed. She was instantly at Sasuke's side, clamping herself to his arm. He roughly shook her off without any hesitation. This was no time for coddling a frightened girl.

The pinkette's scream woke Naruto up. He repeated Sasuke's earlier actions, except with a kunai and a shout of "What the Hell?". The result was the same though. After the failed attack, the creature dropped to the ground and stood up straight, displaying its staggering two meter height to the children.

"_Now that you are all awake, how did you three find this place?" _Naruto's jaw dropped.

"Did that freaky thing just talk?"

"W-we were in a forest clearing wh-when we found the entrance and d-decided to look around." Sakura was able to stammer out as she cut Naruto off before he could say anything that would make the thing mad. The creature frowned.

"_We were not meant to be awakened yet. Your exploration has set things in motion which cannot be undone." _By now, Naruto's courage had returned, and he pointed an accusing finger at the anthropomorphic cat.

"You're mad at us for waking you up? You're the one who made this place so easy to get into and then attacked us for no reason." The blond jinchuuriki shouted, but his previous confidence withered under its harsh glare.

"_This vault was hidden deep below a dense forest, with the only entrance being through a two-inch thick steel door, as well as multiple psychic barriers in place throughout the facility to prevent the random passerby from stumbling into here. If they are still able to gain entry, my semi-conscious self would continually place powerful suggestions within said person' s mind to leave, while also manipulating their memory in order to assure them they were simply here in a dream. Should all else fail, a full scale mental attack would be unleashed upon the intruder to disable and forcibly remove them from the area. Not only were the three of you able to bypass every countermeasure, you did so using something that should no longer exist." _Sakura hesitantly rose her hand up, like she was asking a question in class.

"What was it that we used?" She quietly asked. The creature looked up towards the ceiling. Memories of a time long gone flashed through its mind before it answered.

"_The Power of Dominance. The ability to control Pokémon."_

The statement was underwhelming for the genin, for they had no idea what that was. Seeing their confused expressions when it looked back at them, the monster continued to speak.

"_Do you know what a Pokémon is?" _Each shook his/her head no, so he elaborated. _"Long ago, creatures known as Pokémon once roamed this world. I am Mewtwo, the Genetic Pokémon." _Mewtwo's eyes flared and three forms were carried from the beds and set in front of the psychic. Among them was the orange reptile Sasuke had seen earlier. He indicated at that one first. _"This is Charmander, the Flame Pokémon," _The middle one was on all fours, with a stubby little tail at the back and a strange off-white color to it. Around its neck was ring of tiny, green bumps. Sprouting from the top of its head was a large leaf. _"Chikorita, the Leaf Pokémon," _The last one on the right also had four legs, but was blue and had a large fin for a tail along with one on its skull. It had odd, orange projections on its cheeks. _"And Mudkip, the Mud Fish Pokémon."_

"What does this have to do with the power you were talking about earlier?" A hint of annoyance found its way into Sasuke's voice.

"_Had it not been for them, all of you would have died." _Each child's eyes widened at that._ "You three awakened the power inside of you to halt my mental assault. However, the Power of Dominance can only be used on Pokémon who have acknowledged you as their partner. After using its strength for the first time, my body rejected your hold on it. That left the power with nothing to anchor and stabilize itself too, so it began to drain from your bodies, searching for anything that it could bond with. There are only nine Pokémon species in existence able to instantly forge a connection between themselves and a human. By your actions this day, for the first time in a thousand year, humans and Pokémon are now bound together once again."_

XXX

Deep within Naruto, a beast stirred. The Kyuubi cracked open a massive eye , roused from its slumber by Mewtwo's onslaught. Anger surged forth at the sight of a cage door in front of it. The tailed beast let loose a roar and slammed a mighty paw against the bars. Onward it raged, crashing against every side of its new prison, refusing to accept the futileness of its actions. Eventually the fox calmed as the burning fury turned back into a cold hatred.

Now level-headed, the nine-tailed behemoth started exploring its new jail, testing the limits of the seal. It soon discovered that the dregs of its chakra leaking out allowed the beast to access its host's memories and senses. The Kyuubi looked through the memories first in search of anything it could exploit. What it found in the most recent ones caused a massive grin to appear on the monster's face.

"**So, this brat has discovered the last remains of my former kind. Hmm, perhaps he won't be as pathetic a meat bag as I thought."**

XXX

**And cut! Now comes the mandatory Author's Note.**

**First off, don't worry. I know how much you guys love explanations, so next chapter will have even more of them. Next, this story will only feature Pokémon from Generations I-III. I can't handle any more than that, I'm just one person! As for fighting, it will be fast paced and unique like the manga, but not quite as bizarre *cough*Jynx Ice Dolls*cough*.**

**I guess I should mention that while The Dark Void will be occasionally be helping me with this, it will mostly be my own story. That's all for now folks,**

**Sincerely,**

_**Glock3bb**_

**P.S. I'll give a shout out to the first person who guesses the reference in this chapter. Hint- its from a video game. No, its not **_**Pokémon, smartasses.**_


	2. Discovery Part II

**Yesssss, Yessss. My plan is working perfectly. First, Pokemon Conquest will be a major success, and then I will be able to create a true Naruto/Pokemon crossover. Mwahahahahaha!**

**To bad I don't own either one of them and that I have no real control over what direction each series goes in...Or do I?**

**No, I don't...Mwahahahahahahahahaha!**

III

"_Come, there is much I still must teach you and little time to do so." _Mewtwo ordered as he glided out of the room. Naruto, Sasuke, and Sakura looked at each other but stayed in the same spot. All of them were in a slight daze, still not quite being able to comprehend what they had just been told. Their new companions, however, were not and began tugging at their respective trainer's legs. This was able to wake them from their stupors enough to follow. They exited the living area into the central pavilion and joined Mewtwo in the middle of the room.

"_Before we begin, I would like your permission to examine each of your minds. I wish to know how much the world has changed during our slumber." _Naruto looked at the Pokémon quizzically.

"If you can look into our heads, why didn't you just do it instead of asking?"

"_The mind is a sacred place." _Mewtwo lectured. _"For every being, it is the final refuge where they can retreat to escape the outside world. My psychic powers may grant me the power to peer into there, but I refuse to exercise it upon those who are unwilling and have not given me reason to do so. Therefore, I ask again; will you allow me to look into your minds?"_

"Well, if you want info about history and things like that, you should probably read Sakura's and Sasuke's minds, not mine. I was never really good at that kind of stuff." Naruto said while chuckling in slight embarrassment, rubbing the back of his neck. He hated having to admit to that. However, the other option was not something he really wanted either. There was a very big, furry secret he himself had just learned of, and he did not like the idea of a creature he had just met learning about it. Mewtwo saw the boy's apprehension and decided not to press the matter.

The Genetic Pokémon turned towards the other two in the group for their answers only to get a flat no from Sasuke. Luckily, the girl was willing, but he had hoped that all three would agree. Even if they had no new information, they would have helped reenforce the accuracy of what he did learn.

Sakura was about to ask what she should do when she felt something touch her mind. At first she panicked, remembering what had happened the last time she had felt something like this, but she took a few deep breaths to calm herself. Once she had done so, other memories began flashing in front of her mind's eye. Most of them were of lessons from the Academy, though there were few others, such as various conversations she had had with her parents. This continued on until everything went white, and the next moment she found herself back in the underground room. Naruto and Sasuke were standing by her sides looking bored, while Mewtwo was before her, his eyes closed in concentration.

"_Hmm...Thank you, Sakura. This knowledge will prove to be most helpful." _Sakura blushed slightly at the small praise. _"Your first lesson will be about the history of Pokemon, next will be general tactics and type advantages. After that you will learn how to utilize the Power of Dominance properly. Finally, I shall teach you how to fight with your Pokémon." _Looking down at his own Pokémon, Naruto did not feel filled with confidence.

"Are you sure about that? The fighting, I mean. They don't really look all that strong." Apparently Mudkip took offense to this as he jumped up and smacked Naruto across the face with his tail fin. The blond reeled back slightly with a large red mark on his cheek.

"_Thousands of years of natural selection have instilled every Pokémon with the innate ability to fight." _Mewtwo started, using the incident to begin instructing. "_This trait is one of the reasons our species were became intertwined. Humans would chose Pokémon to help fight with them in their own internal disputes to devastating results, and the Pokémon would often be given food and shelter in return for their support. _

_It was during these dark times that the first method of 'catching' Pokémon was created. By themselves or with the aid of other Pokémon, humans would over power Pokémon in the wild and force them into containers designed to hold them. It was soon discovered that once a Pokémon had been caught in such a way, it became more docile and was more willing to follow the orders of the one who had captured it. The ancient Pokémon acknowledged their captors strength and agreed to stand with them. This was the basis for the Power of Dominance. A person able to accomplish such a feat was given the title of a Pokémon Trainer. The technique for capturing quickly spread, and soon every nation had a large number of trainers constituting their armies and law enforcement. These trainers quickly became the hearts of their countries, _

_With this new advancement came a problem, however. Trainers soon began to desert their kingdoms, for they were unwilling to see their partners die in the unending battles. The desire to fight is powerful though. Trainers and their Pokémon became restless, wishing to pit their strength against others but without the chance of losing their comrades. One day, a large group of the deserters found a solution. Together, they formed their own league of trainers. Members of this league would do battle against each other but only until one's Pokémon could no longer continue fighting. The killing of Pokémon was strictly banned for members and severely punished. After many years of wandering, the League finally found a place of refuge in the Indigo Plateau, a place not yet claimed by any kingdom due to the might of the wild Pokémon living in that area. Once a year, every trainer within the League would gather there and fight in a large tournament. The winner was crowned Pokemon champion and recognized as the strongest trainer in the lands. Life as a trainer was not an easy one though. _

_The loss of most of their Pokémon trainers was a serious blow to every country. Any trainer that refused to be a part of a country's army was hunted down, the leaders fearing the strength they could achieve. The only safe haven for them was the plateau where their annual tournament was held. This became the center of the League; the sheer number and power of the trainers located there discouraging any outside attacks._

_Ultimately, anarchy began to break out across the world. Nations no long had the means to expand their large borders, let alone maintain them. In desperation, the numerous lands held a conference and agreed to end hostilities in the hopes that the exiled Pokémon trainers would then return to their countries. Most did, having missed their homes in their banishment, but a few remained behind at the plateau to maintain it for the next tournament._

_Though the wars over land and resources were finished, Pokémon remained a staple part of human society. Many Pokémon have skills that are beneficial outside of the field of battle, and your kind's loyalty to their partners in life was unshakable. The return of the trainers and the end of conflicts ushered in a golden age, fueling massive advancements in technology. Some trainers set up state-funded hospitals for humans and Pokémon alike. Others established gyms to pass on what they had learned to the next generation. Many returned to their jobs as peacekeepers. They lent their aid to the local police forces of their native countries, eventually regaining their role as the main branch of them. A small number turned their attention towards studying Pokémon and finding out everything they could about their friends and comrades._

_The science of capturing improved by leaps and bounds, culminating centuries later in the pok_é_ball, the round devices you saw earlier. With their invention, the number of trainers increased exponentially due to them being cheap, portable, and easy to use. Becoming one was no longer considered an honor; instead, it was a rite of passage. Upon turning ten, children would be given their own Pokémon and sent out on journeys to prove their worth. Most of these new, younger trainers chose to do so by challenging the various gym leaders, hoping for the chance to participate in the Pokémon League championships of their continent, but this was not always the case. Others did so through breeding or capturing rare and/or many different types of Pokémon. A trainer could also chose to become a disciple at one of the various gyms, dedicating themselves to the teachings of their leaders. _

_It was during this new age that researchers first discovered the existence of the Power of Dominance. Originally, it was thought that a Pokémon's willingness to accept the orders of its trainer were merely based on its personality."_

"What does all of this have to do with us, and why should we care? Just start teaching us how to use them to fight." Sasuke suddenly interrupted. That was the only part that he cared about, and he was not the only one. Sasuke at least had tired to stay focused in case anything important came up, but Naruto had been zoning in and out from the start like he used to do in the Academy. In fact, Sakura was the only one who was still really listening, having been engrossed by what Mewtwo was saying. The Genetic Pokémon shot the Uchiha an icy glare that caused a chill to run down his spine.

"_This is your heritage. As the first Pokémon trainers in this new world, it is your duty to understand where the legacy of those who came before you. The Power of Dominance is not some trifle talent to be used like a simple tool until it inconveniences child. It is the manifestation of the bond forged between humans and Pokémon through the fires of war and the stillness of peace over multiple millennia. By their own volition, the Pokémon next to you saved your lives by choosing you as their new trainers. Should I see even a hint of you abusing this power, lording over them as a master does his slaves, you shall learn a new meaning of pain." _Mewtwo's voice was now ringing in the heads of the three genin, his eyes lit up once again while he floated above the ground, the air around him quivering with his anger. They took a small step back in fright, but it was unneeded. Mewtwo was already calming himself. He had to remember that the ignorance of these children was not their fault. They knew nothing of the Pokémon world nor the horrors supposed trainers had willfully done to their Pokémon in the past.

"_Very well then. If you are so eager to fight, then we shall commence your battle training at once." _He turned and floated to the back wall near the door that lead to where the children had awakened him. Waving his hand, a panel slid back to reveal a screen and keyboard that Mewtwo began typing various commands into. Naruto leaned over to Sasuke and whispered just loud enough for him to hear,

"Hey Sasuke, next time, try not to piss off the freaky cat with mind powers, OK?" Sasuke just grunted in response, but even he had to admit it was sound advice.

Mewtwo, having completed his business at the console, headed back to the genin. A small twist of his hand triggered the activation of the multiple flood lights on the ceiling, coating the area in a sharp glare.

"_Typically, Pokémon battles would consist of an individual or pair of Pokémon facing off while receiving instructions from their respective trainers. This is because most trainers severely lacked the strength and stamina required to participate in the fights themselves. However, the world has changed, and the path of the shinobi is one of constant struggle. You three will not have the luxury of directing from the sidelines. In the end though, that may prove to be more of a boon than a bane. The Power of Dominance was first formed in the midst of battle, so come, find that strength and fight."_

With those finale worlds, Mewtwo sent out a telekinetic blast that rippled the air around it. Naruto, Sasuke, and Sakura hurriedly jumped out of the way, their Pokémon following right behind them. Naruto grinned knowing this was his chance to show his stuff.

"You ready for this?" He asked looking looking down at Mudkip. Getting an exited nod in response, Naruto brought his hands up and formed a cross shape with his fingers. "Alright then, let's do this. Kage Bushin no Jutsu!" Naruto cried out, his side of the dome suddenly filling with replicas of the orange-clad ninja to the surprise of everyone else there. "We're not done yet, Henge no Jutsu." Smoke erupted from the collection of clones; its density hiding whatever Naruto's plan was.

"Charge!" From out of its depths came a mass of Naruto and Mudkips. Together, they all ran at Mewtwo, Naruto intending to take him out with sheer numbers just like he had Mizuki. Mewtwo stood firm and crossed his arms over his chest. When the clones' attacks were just about hit, he threw his arms out to the side and unleashed a powerful psychic wave. An unseen force expanded out from him and sent front rows of aggressors flying back into the other waves. The clone army was disoriented for a moment by the counter, giving Mewtwo time to go on the offensive himself. Raising a hand, he grabbed one Naruto and Mudkip out of the crowd with his powers. He held them suspended in the air then began to speak.

"_An interesting technique, but futile against me. Your clones all have a thought pattern distinct from the real Mudkip and you." _Mewtwo flicked his wrist causing the two to crash through the other clones, dispelling them while the originals took blow after blow. Some of the clones charged forward again to try and hit the Genetic Pokemon, but he just redirected his improvised weapons to take them out. Once all of the Kage Bushin were gone, Mewtwo's eyes flashed, slamming the helpless trainer and Pokémon into the far wall from him, finally letting the two to fall to the ground.

A low rumbling was heard the second after he did so. The ground around the group began to tremble harshly. Sasuke and Sakura looked around, not knowing what was happening. Slowly, crystals began to form on the outer edges of the ring, creeping forwards to the center until the entire room was covered in a thick sheet. Large, spiked mounds of ice began pushing up out of the dirt within the lines, ascending towards the ceiling. Soon the entire arena had transformed from a plain field into a glacial mountain range.

"What just happened?" Sakura asked.

"_This arena can be changed to mirror a multitude of different battlefields. Be prepared to fight on any terrain, for it may change at any time."_ Mewtwo answered them, standing peacefully upon the tallest peak in the middle of the room. Seeing his opponent, Sasuke took off to enter the fray. Behind him ran Charmander, trying to keep up with his new trainer. Sasuke weaved through the crevices between the individual eminences. He finally reaching the center and started scale its face. The mountain's side was steep, and the fact its whole mass was ice made it all the more treacherous to climb. During his climb, the Uchiha heard a shout from behind him, indicating that Naruto had finally recovered and was returning to the fight. The knowledge caused Sasuke to push on even harder, refusing to let the loser catch up with him.

The raven-haired boy was now close to the summit. He secured his feet along a small ridge of ice and leaped into the air at his target. Sasuke contorted his body so that his feet were leading him, intending to kick Mewtwo where Sasuke guessed his center of mass was. Before he connected though, he was hauled up by his ankle and left dangling in front of the legendary.

"_Attacking mindlessly is a fool's plan. You left behind your teammates to fight on your own. You are not even trying to work with your Pokémon in this battle." _Sasuke glanced downward and saw Charmander far below him, working hard to climb as fast as his short arms and legs would allow him. Mewtwo released his hold on the child causing him to fall and slide back down the icy slope. He collided with the Fire Pokémon along the way until both hit the bottom of a nearby butte. Naruto and Sakura had reached him by now, and the pinkette offered a hand to help him up which was ignored. _"In the end, that is what a Pokémon battle is. Two sides working together to overcome their opponent. Only by working in tandem with each other are humans and Pokémon able to attain their true potential as a team. The Power of Dominance is only a tool used to achieve this goal, but you are not even using that. Focus your minds; reach out and feel the bond between you and your Pokémon"_

Once again, the earth started to shake and stir. The ice around them began to melt away, quickly being reabsorbed back into the ground. The temperature began to rise rapidly. In place of the glaciers, the blackened and charred remains of trees pushed through the dirt to stand looming over the genin. Small fires came to life all around, further heating up the air. Mewtwo was now at their level, standing at the entrance of the scorched remains of a house.

Apparently Mewtwo's had little affect on the male ninja, for as soon as the terrain settled, Naruto and Sasuke rushed at him. Though this time they did seem to be at least trying to work their Pokémon into their attack patterns. Sakura was about to run forward to try and help in some way but was stopped when Chikorita grabbed the bottom of her skirt in her mouth. Sakura looked back at her partner.

"What is it...um...Chikorita?" She said, not quite sure how to address the Grass-type yet.

"Chika Chika." The Pokémon chirped while smiling. Sakura just stared at her.

"Ummm..." Sakura puzzled over what her Pokémon was obviously trying to communicate to her. She remembered what Mewtwo had just said and decided to give it a try. Closing her eyes and crouching down next to the female Pokémon, the young girl emptied her mind in an attempt to feel what the Psychic Pokémon had been talking about. She became of aware of a sensation in the back of her mind, tugging her thoughts in that direction. Sakura mentally reached for it and let out a small gasp. She felt, something. She did not know how to describe it. It was almost like she could hear another being's thoughts in her head, but not quite. They were jumbled together with emotions and instincts; feelings and desires combined into one ever shifting conglomeration. And then there was the power. It coursed through her entire body, tingling the tips of her fingers and toes. The power rang in her mind, echoing of great age and majesty. It empowered and guided her, pulling the girl deeper into its embrace.

Sakura's eyes snapped open and she gulped down air as fast as she could. That moment had ended all to soon for her, but she could still feel it somewhat, floating around the edges of her consciousness. Naruto and Sasuke came hurling to the ground next to her; their duel attack had little success it seemed. Sakura stood up and turned to face Mewtwo. She could feel Chikorita urging her to go for it in her head.

"Are you sure?" She asked, and the Grass Pokémon nodded firmly. Sakura took one last deep breath before running right at Mewtwo. Chikorita was by her side the whole way. The distance closed, Sakura reared back her fist and put all her wait into one punch, swinging directly at Mewtwo's head. "Chikorita, Tackle." She called out instinctively at the same time. Chikorita jumped into the air and turned her body to slam into Mewtwo with her left shoulder leading. Both attacks were stopped cold a foot away from the legendary's body by a psychic barrier.

From behind her sprung Naruto, Mudkip, Sasuke, and Charmander, each trying to break the invisible wall between them and Mewtwo. Mewtwo's eyes flashed and all six were picked up. Slowly, they began to spin around him, steadily gaining speed with every rotation. The group whirled about, their torment eventually ended by a massive shock wave that sent them all flying outwards from the psychic. Their flights were shortly ended mostly by whatever object they happened to crash into. Sakura grabbed Chikorita in the air and held her against her chest. The two were lucky and simply hit the ground, rolling across the hard dirt before coming to a stop.

Sakura stumbled to her feet, scrapes and bruises showing on her skin wherever her clothes did not cover. Chikorita squirmed out of the hold Sakura had on her and dropped to the ground.

"Rita, Chikorita." She said quickly. Sakura shook her head and tried to figure out what she meant. The did not appear to be anything wrong with their link, but the words Chikorita and the Power were influencing her to say did not make much sense. She decided to go for broke and trust her partner.

"Razor Leaf." Sakura yelled, pointing a finger at Mewtwo. Chikorita whipped her head in a circle, the leaf on top following just behind. From out of that leaf, four other crescent shaped leaves appeared, slicing their way towards the Genetic Pokémon Mewtwo quickly reconstructed his psychic bubble to guard himself. The razor sharp blades hit, but rather than coming to a dead halt, they were sent careening of to the sides. The leaves easily tore into the burnt husk Mewtwo was standing just underneath and out the other side. While the attack itself failed, it did enough damage to the house to bring its remains tumbling down onto the psychic. Sakura pumped her fist, having finally been able to damage their opponent.

Her victory was short lived, however, for from within the smoldering ruins came a massive blast, sending debris scattering about. At its epicenter stood Mewtwo standing straight up, completely unharmed. He held up a hand, but before anyone could make another move, a loud chiming was heard. Mewtwo's posture relaxed, the earth around him gradually swallowing up the fiery stage.

"_That is enough fighting for now. Come, we shall tend to the wounds of you and your Pokémon Then we will continue with your other lessons." _The abrupt end was a not unwelcome surprise to the newly minted trainers. They trudged to where their newest teacher was heading, wondering just what they had gotten themselves into.

III

**And, cut! So, yeah, I meant to get this thing out sooner than I did, but I was not able to. I guess my plan to run around the Earth so fast that its rotation is reversed thereby turning back time still has a few flaws in it. Damn, back to the drawing board then.**

**Not much else to say this chapter, just that I hope you all liked it, and thanks to The Dark Void for finally getting my ass in gear.**

**See ya,**

**Glock3bb**


	3. Discovery Part III

**The chance of me ever owning Naruto and/or Pokemon is like the mass of an electron, so small that it is basically non-existent.**

III

Steam gently wafted past Naruto's pajama clad body as he exited the bathroom of the underground complex. He stretched his arms and let out a content sigh, glad to have the dust and sweat of a hard day's training off his skin. The blonde walked out into the bedroom area where he had awakened earlier yesterday afternoon. There, Sasuke laid on his back upon the farthest mattress from the washroom with his hands behind him beneath his pillow. Charmander was curled up tightly on the floor near his trainer's bed. Sakura sat leaning against the headrest of the bed next to the Uchiha while she calmly petted the Chikorita snuggled in her lap.

With hardly a moment of hesitation, Naruto ran and belly-flopped onto his own bed. The subsequent bounce allowed him to reorient himself so that he landed cross-legged and facing his teammates. Mudkip, whose sleep had been interrupted by said action, shot out from underneath the mattress and tackled the newly minted Pokétrainer to the ground. The two partners began to wrestle on the floor, their laughter and other sounds of glee filling the room. Sakura huffed and glared at them.

"Naruto, quit fooling around. We need to get some sleep." They definitely needed it what with the day and a half the three just had. After Mewtwo showed them how to operate the strange, dome shaped machine they had seen earlier, he brought them food to eat while they waited for their Pokémon to heal. Apparently, the facility was meant to house humans as well as Pokémon in case of emergencies and therefore had been stocked with almost everything the three would need. It was surprising that it was all in good condition considering it had been down there for over a thousand years.

Once the Pokémon were done recovering, Mewtwo spent the rest of the day drilling them into the ground. They fought for hours, yet none of the genin nor they Pokémon were ever able to get a clean shot on the legendary. Mewtwo eventually called a halt to the combat and let the children eat supper while he began teaching them basic information about Pokémon. That continued until what they guessed was night time, and the six were sent to bed. The next day was roughly the same schedule, battle for awhile, then eat while the psychic lectured them.

"Oh, come on, Sakura. We're just playing around." Naruto said in between snickers. Mudkip had managed to grab a couple of his sun-kissed locks in his mouth and was lightly tugging at them.

"Idiot, we're not here to play. We're supposed to be training." He said simply waving off her chiding.

"Yeah, yeah. But it's not like learning to use that Power of Dominance thing is that hard." Sakura's gaze bore into him even harder at his comment.

"If it's so easy, why haven't you been able to use it yet?" Naruto was caught off guard by her question and floundered to come up with a retort. Sakura smirked, and Chikorita tittered at his expense. He pointed an accusing finger at Sasuke.

"What about him? Sasuke hasn't been able to do it either!" Sakura flipped her hair over her shoulder.

"Sasuke probably hasn't tried yet. I'm sure he could do it the very first time if he wanted to." The blond in frustration at his teammate.

"Fine, you want me to do it; I'll do it." He jumped up off the floor back onto his bed the way he was before. Grabbing Mudkip at the same time, Naruto set his Pokémon in front of him and, after a short grunt, focused every ounce of his concentration on connecting to his new partner. The mud fish Pokémon stared back at the trainer sitting across from him with his head cocked to the side in a puzzled expression. The two remained in that same position, never moving a muscle. Sakura watched them intently, waiting to see what would happen. Even Sasuke sat up to pay attention.

Over a minute passed by, suspense building in the air. The entire room grew still like the calm before a storm. Two minutes passed. Sakura shooed Chikorita out of her lap and cautiously got up from her bed. She approached Naruto in three slow, carefully planned out steps. Standing beside her teammate, the pinkette paused for a moment, then smashed her fist down upon his head.

Naruto's torso snapped forward from the blow, but he instantly sat back up, gulping down huge amounts of air. His navy blue face quickly returned back to its normal color in response to the oxygen flooding back in to his system. Mudkip looked back and forth between the two teammates, still trying to understand what was going on.

"You moron! You're not supposed to stop breathing!" Sakura shouted in anger. Naruto could not respond as he continued to try and regain his breath. Sasuke muttered something that was incoherent to the others and laid back down on his bed.

"Darn it. Sakura, how were you able to do it so easily?" The young kunoichi was about to smirk and pump her fist in triumph, but she stopped herself when she heard the disappointment and self-doubt in Naruto's voice. It was something she had never thought she would hear. Ever since she first met the boy, Naruto had never once backed down from a task. He always dived head first into every task even if he had little chance of success. The most he ever did was whine a little but even that did not last to long. Sakura looked up at the ceiling with a frown, letting out a small sigh. Taking a second to collect her thoughts, the pinkette looked back at the blonde.

"Its not something you can force, Naruto. You just have to...feel it."

"Huh?" Sakura ran a hand through her hair while she tried to figure out a better way to word what she was trying to say. She soon clenched her fists and stomped a foot in frustration.

"Hrrrgh, just try and do what I tell you." Naruto nodded and repositioned himself so he was facing her, and Mudkip was at his side.

"Close your eyes and relax. Don't think about anything." He grumbled a bit at those words. Naruto had never been one to sit still for very long. Even when he was a toddler, he was constantly on the move. The fact that he now needed to remain sitting in one spot not doing anything was almost torture. The blonde took a few deep breaths and tried to concentrate once more. This time, however, he did as Sakura had instructed and tried to clear his head. The female of Team Seven saw the muscles in Naruto's face gradually loosen up as his mind emptied. She waited a few seconds then proceeded to go on with the lesson.

"Good. Now you should be able to feel a tugging sensation in the back of your head. Focus on that and let it guide you." Unbeknownst to Sakura, Naruto was no longer listening. In his meditation, Naruto's consciousness had been whisked away deep inside of his own mind, where dangers lurked even for him.

III

The sound of slowly dripping pipes echoed endlessly around Naruto as he came to. He propped himself up on his hands and knees then shook his head, dislodging any remaining grogginess within. The first thing Naruto noticed after doing so was that he was in the middle of a shallow, trickling stream. The water was only about an half-inch deep, just enough to wash over the tops of his young hands. The liquid had a strange feeling to it. It seemed to cling to his skin, swirling about the flesh briefly then continuing on its journey.

Putting that oddity to the side, Naruto pushed himself up and observed his surroundings. He was standing inside of a large tunnel, the ceiling about five feet above him. Rusted, cracked pipes obscured the curved walls. Tiny beads of water leisurely gathered together on the metal underbellies before their inevitable fall. The entire area was covered in a dark red glare originating from one distant end of the sewer.

It was towards that side that Naruto felt inexplicably beckoned to. His feet began to move as if they had a mind of their own, bringing him nearer to crimson light. He drew closer to the source little by little. Though the bloody haze, he could just make out an opening to the tunnel. Suddenly, he stopped in his tracks a short distance away from the mouth.

Behind him, a small, white glimmer began to gently glow. Naruto only caught a short glimpse of it before the speck was consumed by the darker rays around it. Curious, the blond turned and walked back to where he had first awoken.

As he did so, the pale light grew in strength. What had once been a speck grew with every step, beating back the harsh red of the other. Soon, Naruto was naught but a few yards away from the source of the new glow, and he began to feel the differences.

The first light was filled with rage and malicious. It hung in the air, smothering anything it touched. The white gleam, however, was solid and impartial. Its rays carried with them the weight of ages. He could tell that this was something that had existed long before he was and would remain far past what he could imagine. Despite this, the light had a strange familiarity to it, like a word he could not remember but was on the tip of his tongue. He crossed the remaining distance between himself and the white orb and gently placed his hands on each side.

The light's brilliance exploded outward as soon as his hands touched, filling every inch of the damp sewer with its radiance. Naruto's eyes widened in shock, but there was nothing he could do. His arms refused to obey his commands, instead staying firmly stuck to the shining orb. Soon, all Naruto could see was white. The light continued to expand, growing ever larger, enveloping him in its grandeur.

III

Naruto's eyes shot open as his mind returned from his journey inward. Every part of his body felt energized. He could almost taste the deep power rising up from within himself. He looked down at Mudkip who was smiling back up at him. Naruto actually feel his partner's joy. The Pokémon had finally found someone he could connect to and bond with. After a thousand years of waiting, he finally had a true partner once more.

Naruto chocked back tears at the emotions he was feeling. Whether they belonged to him or his Pokémon, he did not care. He, too, was overcome with happiness. He had found a friend that he knew would stick by him no matter what, and he silently promised to do the same. Naruto bent over and wrapped Mudkip up in his arms in a warm hug.

Sakura smiled. She could tell the instant Naruto opened his eyes that he had done it. Chikorita nuzzled her neck against the pinkette's legs, and Sakura knelt down to pick her up. Through their bond, Sakura felt the grass-type's happiness for her fellow Pokémon and his trainer. The young kunoichi flipped the light switch next to her bed then tucked herself and Chikorita into their bed. She heard Naruto and Mudkip start playfully wrestling about again to her side but decided to let them have their fun.

On the other side of the room, Sasuke laid quietly in his bed. He had been listening in on the lesson since the beginning. Naruto was not the only one Sakura's coaching had helped, though Sasuke would never admit that out loud. It was a strange feeling for the boy. He had long ago closed himself off from the rest of the world, yet now here he was, sharing a deeper connection with a creature whose existence he had only learned of a few days ago. He felt closer to his Pokémon than anyone else he had met in his twelve years of life.

In the back of his mind, Sasuke could feel Charmander examining him the same way he was. An inkling of mutual acceptance passed between the two at the end of their appraisals. That being done, Charmander climbed his way up the sheets from the floor and coiled up at Sasuke's feet. The Uchiha huffed and rolled his eyes at his Pokémon's presumptuousness but then joined the fire-type in drifting off to sleep.

III

The following afternoon, the genin of Team Seven stood proudly next to each other, their partners at their sides. Mewtwo stood across from the group, observing them with a keen eye. Above them shone the bright lights of the arena. The dome was quite at the moment as the genin waited for their new teacher to speak.

"_You three have done exceptionally well these past two days. Your control over the Power of Dominance and the bond between you and your Pokémon have both grown at astounding rates. I am proud to call you my students," _Sakura and Naruto accepted the praise with beaming smiles while Sasuke did so with a small smirk. _"But now it is time for you to leave this place." _The abrupt turn threw the genin for a loop and sent them reeling in surprise.

"What? Why? We don't want to!" Naruto stammered, voicing the others' opinion for them.

"_It is necessary. The longer you remain here, the more likely it is someone will find this place while they search for you."_ Sasuke frowned at the psychic.

"What do you mean 'search for us'?"

"_Including the time you three spent unconscious after awakening the Power of Dominance, you have been in this facility for three and a half days. You must have realized someone would have noticed your absences by now." _The group was thoroughly cowed. In actuality, none of them had given any kind of thought to such a prospect. They had been so caught up in the thrill of discovery that they failed to think of little else. This realization brought about mixed feelings.

Sasuke mentally berated himself for not realizing such a fact sooner. Even if there was no one he was particularly close to, the disappearance of any clan member was always treated with high priority. It would be even more so if that person happened to be the last surviving member.

Naruto simply shrugged his shoulders, for the most part. Sure, Teuchi and Ayame might be a bit concerned that he had not shown up for ramen in a while, but he did not believe it would go much beyond that. Iruka probably thought he was just busy with missions, and the Old Man was most likely to caught up in doing Hokage stuff to have noticed he was missing.

Sakura was racked with guilt. She had told her parents she would be back in time for supper after meeting with her sensei. They must be worried sick about her, not knowing what horrible things might have happened to their only daughter to make her vanish for over three days. She could not even imagine how she would feel if the situation were reversed. Naruto felt the heaving mode surrounding his teammates and tried to lighten everyone up.

"Heh, I guess we're the ones late for our team meeting now, right guys?" He said scratching his right cheek. Sasuke muttered 'idiot' under his breath and shook his head at the poor attempt at a joke.

"So, if you don't want other people to find out about this place, how are we going to explain where we were the past three days and where our Pokémon came from?" The raven-haired boy asked. Mewtwo raised a hand and called forth three Poké Balls from the Pokémon storage room. The red and white globes stopped and hovered just above chest level in front of the children.

"_You will not need to explain how you found your Pokémon, for they will not be joining you."_

"What? No way!" Sakura yelled, his voice filled with anger. Naruto and Sasuke added in their own protests until Mewtwo had had enough.

"_Silence." _His voice never changed in magnitude, yet the sheer authority in it quieted the children. _"The existence of Pokémon must remain a secret for as long as possible. Should anyone see your partners, they will surely question what they are, where they came from, and if there are any more like them. Therefore your Pokémon must remain here where it is safe."_ Mewtwo's words cut the genin deep because they knew he was right. The best case scenario was that the village allowed them to keep their Pokémon as long as the three revealed where they got them. A spark of inspiration suddenly darted across Sakura's eyes.

"What if we kept them in their Poké Balls? That way, we could still have them with us, but no would see them." Mewtwo shook his head.

"_It would still be necessary to keep the Poké Balls hidden and out of sight at all times. Aside from that, it is far easier to lose or steal a Poké Ball than a Pokémon; therefore, the safest course of action is for your Pokémon to remain here."_ Sakura visibly deflated at Mewtwo's counter. She could not find anyway around his logic.

"_Nevertheless, do not think this means an end to your training. You will return here the moment you have the chance to slip away unnoticed. There is still much that I must teach you three."_ Mewtwo smiled slightly at the sight of Naruto's, Sakura's, and Sasuke's faces. They each had different ways of expressing it, but he could see in each of them a sense of relief and joy at the prospect of reuniting with their partners in the future. A twinge of bitterness crept into his hapiness for the children, as it brought forth memories of his life a millennium ago. The psychic Pokémon returned his thoughts to the present. He had yet to answer his raven haired student's first question.

"_Not far from this facility is a small system of abandoned tunnels. I have seen to it that a plausible amount of food and trash has been moved there and the entrances collapsed. Your henge technique should be adequate to make yourselves look the part. Go straight to your homes and release the jutsu under the guise of cleaning yourselves up. Upon your return to your village, you will tell them that it was there you were exploring when a cave-in trapped you inside. Any investigation your government will conduct of the structure will simply support your claims."_

"But I thought you didn't want people coming near here?" Naruto questioned.

"_Now that I am awakened, the psychic barriers protecting this place have been greatly strengthened. You three shall be the first and last to enter here unwelcomed. Of that, I will personally make sure."_ Naruto chuckled awkwardly at the reminder of how his team was able to, for the most part, walk straight into the supposedly secure facility. _"It is time. You may say goodbye to your partners first before leaving."_

In an instant, Chikorita found herself squashed between her trainer's arms. She struggled against the hold until Sakura felt her distress through their bond and loosened her hug slightly. Chikorita then reciprocated the loving gesture as best she could. The two remained that way for their entire farewell.

Sasuke stared down at his Charmander and nodded. The fire lizard did the same, beginning to understand the strange way his new partner preferred to communicate. The Pokémon had an advantage over others in this department, for their shared bond through the Power of Dominance allowed Charmander to feel the thoughts Sasuke would never voice.

Naruto squatted down to Mudkip's level. He patted the water-type on the head once, then twice, then again and again. He grinned at the sensation of Mudkip's irritation in the back of his head. The blonde continued the action as his Pokémon's annoyance grew. Finally, Mudkip had had enough and bit Naruto's fingers on his next attempt. Naruto yelped in pain and tried to pry the mud fish off of his right hand. Mudkip stubbornly refused to let go, chomping down harder in response. Now it was Mudkip's turn to have a smug smirk at having reversed roles with his tormentor.

In the end, Mewtwo was forced to step in and break the two up from their childish antics. After being separated, Naruto stuck his tongue out Mudkip. Surprisingly, the Pokémon responded in the same manner. They remained that way until both were eventually overcome by a fit of giggles at the situation. Mewtwo shook his head.

"_That is enough. Return your Pokémon as I have should you." _The three shinobi nodded their heads in understanding and grabbed the floating Poké Balls out of the air. Seemingly as one, they squeezed the orb causing a translucent red light to shoot forth from the front and envelop each of their pokémon. The creatures then disappeared inside the balls with a strange whooshing sound. The act done, Mewtwo commanded the Poké Balls back to where he had summoned them from. _"I shall be awaiting your awaiting your arrival."_

With that dismissal, the genin transformed themselves with a henge. Each of them was now covered in grime and dirt, slight tears added to their clothes for further effect. Naruto, Sasuke, and Sakura waved goodbye to their sensei and headed towards the lift that had first brought them here. After one last lingering gaze, the flashing button was pressed, and the three ascended back to the surface.

III

**So our heroes are going back to the real world, leaving behind their new friends. Will their Partners ever join them there? Find out next time, or maybe the time after, or the time after that. Who knows? Well, I do, but I'm not telling so there. Nyah!**

**Not much else to say this chapter. Expect more action next time, which with any luck won't take two months to get out. Yeah, sorry about that. Anyways, here's to a brand new chapter to go with a brand new school year! Glock3bb in the house sucka's. Let's raise the roof and make some noise!...Man, I'm white.**


	4. Consequences Part I

**I do not own Naruto or Pokémon. According to TvTropes, that disclaimer was utterly pointless. My life is a lie!**

**A couple of things before we start. First off, sorry for taking so long to update. Seriously, I promise I will have a regular update rate for my stories eventually. Secondly, as no one has guessed the reference from Ch. 1 yet, I will give you all a hint. No matter what, the answer will be revealed next chapter, seeing as how it has become an integral part of the story. I swear, I did not plan on this happening when I started the story. Anyway, the hint is: While the reference itself first appeared on the Gameboy Advance, the series it comes from first debuted on the NES.**

**Now that that's out of the way, let's go! **

III

It was the day of team assignments, and as was customary, Kakashi had taken his sweet time walking to the Academy. The three o'clock bell that normally signaled the end of the school day went off shortly after he entered the building. He finally opened the sliding door roughly two and a half hours past the appointed meeting time only to find the classroom empty. At first he was actually some what impressed that the children had the gall to walk out on him; perhaps this year would be entertaining. Figuring he should still track his students down and give them the information about their test the next day, the Hatake left to go to each of their residences.

He first checked Naruto's apartment and received no response to his knocking. Deciding to enter anyway, Kakashi walked around back and up the side of the building to one of the apartment's cracked open windows. Upon entering, he found the place to be in about the condition that he expected. Dirty plates, glasses, and various cooking utensils were piled up in the sink, waiting for their owner to clean them. A few random articles of clothing were strewn about across the floor. The trash bin had just recently been taken out, judging from its empty contents. Looking about, Kakashi found neither hide nor tail of Naruto, so he simply found a pieced of paper and wrote down what the boy needed to know. He put it in an envelope and set it on the table before exiting the way he came.

Moving on, the jounin then went to the Uchiha district, and the area was the textbook definition of a ghost town. Abandoned and decrepit buildings sagged earthward as if under immense pressure from the weight of their memories. If one were to look closely enough at the structures, they would be able to make out the faint crimson stains of human blood still smeared on their walls. Broken windows littered the dirt roads with their glass, and once beautiful home gardens were now overgrown thickets of weeds and vines. Rats and other small vermin scurried randomly about the deserted streets in their hurry to hide themselves from the silver haired man.

He continued to walk until he came upon one home that still seemed relatively intact. The lawn was in fairly good condition along with the flower bed that ringed the outside of the house. Despite how well maintained the house was, Kakashi still had to frown at the sight.

There had been much debate over what to do with Sasuke after the massacre. The standard procedure for dealing with an orphaned child was for them to be taken in by their legal guardians, or, failing that, their closest living relative. If said persons were deemed unfit to care for him/her, the youth would be sent to one of Konoha's orphanages. However, in this case, none of those options were viable. Every other member of Sasuke's family had been killed, and none of the orphanages were equipped to deal with the kind of mental trauma the boy had suffered.

To complicate matters even further, everything the Uchiha clan had ever owned was now up for grabs. Since Sasuke was a still considered a child in the eyes of the law, he could not rightfully inherit his family's possessions and assets. This left all of it in the hands of the village government, which had no use for a vast majority of the items.

That, of course, did not include the hundreds of jutsu scrolls and other secrets the Uchiha had been keeping to themselves for centuries. The Uchiha library, by the very nature of the clan's Kekkai Genkai, was massive. Many of these techniques would be extremely dangerous if they fell into the wrong hands. Of course, every clan had contingency plans in case something were to compromise the integrity of their clan techniques, but none had ever expected anything as drastic as the Massacre.

In the end, it was decided that the boy would be emancipated, allowing Sasuke to take ownership of everything. His relative's assets would be enough to support the young man to until he could do so on his own, and a pair of chunin were tasked to watch over him from the shadows in case anything should happen.

Kakashi sighed at the thoughts. There were no real right answers in that kind of situation. One could only make a choice and hope everything worked out for the best.

On that note, the jounin continued on. His knocking was once again ignored at the front door of the house. This time, though, he somewhat prepared for that to happen and once again slipped in through an unlocked window. He could understand if the boy wanted to spend as little time as possible in the deserted district.

Inside, Kakashi found a home that was very clean and organized. It appeared that Sasuke, while not bad at maintaining the exterior, was much better at keeping the interior nice and tidy. There was not a single thing out of place in the entire house; even the boy's bed was made up perfectly. He quickly wrote another note, but this time he gave it to one of the chunin outside. Their mission had long since been deemed as complete, but the two guards continued to faithfully safeguard the scarred boy whenever they were able to.

It was at the last house Kakashi visited that the door was finally answered. Sakura's home was located near the center of Konoha like most civilian houses were. Such a set up helped prevent noncombatants from being endangered should an invading force ever breach the walls. It also made it easier to evacuate civilians into the protected cloisters underneath the Hokage Mountain. The house itself was a rather small split-level with practically no lawn. The outside was a homely beige color, and the two upper windows were bordered in a darker brown.

Answering his light raps was a woman who was roughly in her mid-thirties. She wore a sky blue sundress underneath a white apron that complimented her cream colored skin. Her hair was the same bright pink as her daughter's, though not as long, only falling down slightly past her shoulders. The bubblegum locks were pulled back behind her head in a high ponytails. Her eyes were a deep, dark hazel. As the air from inside the house slowly drifted out, Kakashi smelled the distinct scent of desserts being baked.

"Hello, can I help you?" Sakura's mother asked the jounin. Her confused tone made sense as the two had never met before.

"Yes, my name is Kakashi Hatake, and I am your daughter's new sensei. Is she here?" The woman shook her head.

"No, she left early this morning to go to team assignments, and I haven't seen her since. Why? Is something wrong? She told us she would be back between one and two, but we haven't heard from her at all." A note of worry was starting to worm its way into the woman's voice. That was exactly the answer Kakashi did not want to hear.

While he could pass off Naruto's and Sasuke's absences as him simply not visiting at the right time, Sakura's file had stated she was a very well mannered girl who was very close to her family. More likely than not, she would have stopped by to at least tell her parents if she were going somewhere else. The fact that she had not and her mother's growing anxiety over that fact caused warning bells to begin going off in his head.

"Mrs. Haruno, would it be ok if I waited here for her? Certain events caused me to be late for the team meeting today, and I information your daughter needs to know concerning the next few days." The elder pinkette stood aside, ushering the jounin in.

"Yes, of course. Do come in." Kakashi nodded his head graciously. Before entering, he quickly created three shadow clones. Two were ordered to go and wait at Naruto's and Sasuke's houses in case either of them showed up there while the final clone would search around the village for his absent team. The woman was startled by his actions but did not say anything.

He stepped through the doorway, slipping his sandals off on the mat, and Mrs. Haruno led him through the house to a small dining area. On the right side, a waist high counter acted as a partial divider between the kitchen and the dining room. Said counter was covered in an assortment of baked goods having been set out to cool. The silver haired jounin took his place in a corner of the dining area while Sakura's mother returned to her cooking. Even without years of experience in reading people, Kakashi could tell she was growing more anxious by the second.

Soon, the sun began to set, casting out its final golden rays. Mrs. Haruno had retired from baking to finish sowing a dress she had been making for her daughter as a graduation present. Kakashi still stood motionless in the corner he had claimed earlier in the day.

Suddenly, the front door to the house creaked open, and both of their heads snapped towards it. In walked a man just over six feet tall. He was wearing a dark, pale blue kimono shirt that hung loosely about his torso and a fern green under robe. His simple, brown shorts stopped slightly above his knees. Short, brunette hair covered the man's head.

The man froze at the sight of Kakashi but quickly took it in stride. He gave his wife a quick peck on the cheek when he passed by that she half-heartedly returned. Turning his attention back on the jounin, Kakashi answered the about to be asked question.

"Mr. Haruno, I presume?" He nodded in affirmation. "I am your daughter's jounin sensei. Have you had any contact with her after she left for team assignments earlier today?"

"No, I havent. I thought she'd be back by now." Mr. Haruno said in a surprisingly deep voice.

"She isn't. Mr. Hatake has been searching for her and her teammates since he found them gone from the academy." Mrs. Haruno explained. Her husband's face became stern at that news. He grabbed a chair and sat down next to his wife, taking her hands in his. His large hands dwarfed hers by a fair amount, but he used that to his advantage, gently stroking the back of his love's palms with his thumbs.

Hours passed. Darkness now covered the village with no sign of the missing Haruno. By now the vast majority of Konoha was asleep comfortably in their beds, and still the three were waiting. None of the shadow clones Kakashi created had dispelled yet, so they had not found any hard evidence of where the children had gone. Finally, Kakashi had to admit he could not wait any longer and canceled the jutsu.

Memories from the three doppelgangers came rushing back into his mind. The clone out searching the village had run into a group of chunin who were also looking for his three genin after they apparently tried to booby trap one of the western guards towers with itching powder. Kakashi's uneasiness grew just as his clone's had a few hours ago. If that was what the three had been up to after leaving the Academy, then surely they would have returned back to their homes by now. Sakura might have gone to a friend's house until the situation cooled of, but sadly for Naruto and Sasuke, that was an unlikely possibility. All of these facts meant there was only one thing left to do.

"Mr. and Mrs. Haruno," Kakashi tried said as calmly as possible; it was to no avail as the two still jumped at the sound. Mr. Haruno was as stone faced as ever while Mrs. Haruno was struggling to maintain her composure. "I must ask that you to come with me to the Hokage Tower. We need to report that your daughter and her teammates have gone missing."

That was the final straw. The frightened mother broke down sobbing, her tears staining the fabric in on the table. Her husband pulled her in close, and she continued to cry onto his shoulder. Kakashi remained standing in the spot feeling uncomfortable. He had never been good at consoling others, but luckily Mr. Haruno was here to do that job for him.

For over ten minutes Mrs. Haruno bawled until her husband gently helped her to her feet. She clung to his side as he guided her out of the house behind Kakashi, locking the door behind them. Kakashi guided the two down the dimly lit streets towards the Hokage Tower. Their pace slow but steady.

Fortunately, Kakashi's status as not only an elite jounin, but also a close friend of the Hokage allowed the group to head straight through to his office after only a basic security check. Of course, the Hatake knew there was more to the process than just that, but there was no need to inform the Haruno's of the four ANBU carefully observing them from the shadows.

The fact that the aged leader was still here, burning the midnight oil was no surprise to Kakashi. Hiruzen could have easily been done with what all was needed of him by this time of night, but always made sure to have at least an hour free every night. The reason for this was that the old man would use that time to visit every one of Konoha's hospitals and talk with the sick and injured there. It was one of the many reasons why the Third was so beloved by the Leaf's citizens.

When the three entered the Hokage's office, they found the elderly man already staring intently into his crystal ball, having been immediately briefed on the situation. Mrs. Haruno opened her mouth to address her leader, but Kakashi put a hand on her shoulder and shook his head. Minutes passed. The frown on Sarutobi's face grew ever more pronounced. After what seemed like an eternity, he looked up from his work with a forlorn look in his eyes.

"Kakashi, go to the Inuzuka compound. I have sent a message for all off-duty clansmen to join you in a search effort. Any available Hyuuga will also be joining you as soon as they can. I want these children found immediately." He commanded, his voice like hardened steel. The jounin nodded once in understanding and disappeared into a cloud of smoke. The Hokage then turned his gaze to the two civilians left before him.

"Mr. and Mrs. Haruno, do not worry. We will find your daughter and her teammates, but right now I need your help. Kakashi sent a message ahead of you, informing us of what he had learned, but we need more information. I need you to tell me everything you can about what your daughter said, where she might have gone, and anyone else who may know something."

And so the search began. For three days, the shinobi of the Leaf were in a suppressed uproar. Search parties combed every inch of the village and the surrounding area. The intelligence division was hard at work not only trying to find any and all possible leads but also working to prevent the spread of the news to other countries. Security was tightened all across the Land of Fire. Even the ninja Sarutobi had placed to monitor Danzo reported that Root was conducting its own investigation into the matter, though the Third Hokage was sure it was not for the same reasons.

By the third day, Kakashi was weary from lack of sleep and nourishment. His chakra reserves were running dangerously close to empty. The only thing keeping him going were the soldier pills he taken the day before, and yet he could already feel the temporary boost fading, along with his hope.

It seemed to Kakashi that no matter what he did, he was doomed for failure. He failed his father by renouncing the man after his suicide. He failed Obito and was forced to watch him die at Kannabi Bridge. He failed to protect Rin like he had promised to and was forced to kill her. He failed to help Minato-sensei that fateful night the Kyuubi attacked.

These thoughts plagued Kakashi's mind as he did anything he could think of to try and find the missing children, but with each passing day the chances of finding them dwindled. It became more likely that he would have to add even more people to his list.

It was shortly past noon on the fourth day of searching that Kakashi received the news he had been longing for. He was in the process of making another round outside the perimeter of the village when, high above, a messenger hawk screeched. The jounin stopped running and held out his left arm. The bird landed with hardly sound and waited while Kakashi undid the message. As he read the news, he had to fight to keep his emotions under control, and the Hatake made a silent prayer of thanks to whatever deity had decided to give him a second chance.

III

Kakashi mentally sighed as he looked at his newest genin team. The late afternoon sun was halfway through its decent to the treeline, causing deep, lengthy shadows across the forest. All four were gathered at the center of Training Ground Seven the three days after the three had reappeared. No other genin team had ever caused the gray haired jounin as much stress as these three had, yet this was the first time he was meeting them in person.

After getting word that his students had been found, Kakashi had gone straight to the hospital where the note said his students had been sent. He checked in on each of them and introduced himself. The conversations were brief but long enough for him to be sure they would be ok. He then when straight to the Hokage's Tower to find out what exactly had happened.

While attempting to hide from their pursuers, the three had been trapped underground by a cave-in in a cave that they found in the forest. However, it was not any old cave that they had stumbled upon. No, apparently his students had managed to find one Orochimaru's old, hidden laboratories.

Kakashi had shaken his head at that fact. Fifteen years after he abandoned the Leaf and they were still picking up the pieces of his inhuman experiments. Fortunately, or unfortunately depending on how one looked at it, this lab's contents had been deemed important enough by Orochimaru to be either removed or destroyed before he fled. This tidbit of information meant that Naruto, Sasuke, and Sakura were confined even longer to the hospital as the doctors made absolutely sure that everything was fine with their bodies. The Snake Sannin always had a knack for leaving behind unwanted surprises.

Kakashi forced himself to cut off that line of thought and refocus his mind on the matter at hand. The job of examining what was left in the cavern was left to ANBU and Intelligence department. His was to test these three and find out if they are ready for life as a shinobi.

"Seeing as how we've already been introduced, let's jump right into it, shall we? You three will have until noon to steal these bells from me." He said, holding said the pair of chimes up for them to see then hanging them back onto his right side. "Anyone who does not get a bell will tied to one of those stumps and be forced to watch as the rest of us eat lunch. They will then be sent back for another year at the Academy. Since there are only two bells, at least one of you will not be passing. Do you understand?" The genin nodded."Alright then, one final thing. Come at me with everything you have, or you will never be able to get a bell. Begin!"

Naruto, Sasuke, and Sakura took off the second he gave the signal. Curiously though, Kakashi's honed senses told him they were moving away as a group rather than scattering like a typical team of genin would. Interesting. The silver-haired jounin pulled out his favorite copy of Icha Icha and began his nonchalant pursuit. After all, why should he stress himself when they were the ones that would eventually have to come after him?

Kakashi's walk soon brought him to a small clearing in middle of the thick forest. The soft sound of stirring leaves drew the man's attention away from his book as five Sasuke's and Sakura's along with a horde of Naruto's leaped out of the tree line. He quickly noted that the first two groups of doppelgangers were moving far to fluidly through the air to be real; Naruto's clones, on the other hand, were all to real and ready to prove it.

The Hatake dodged to the left to start the tedious work of dispelling each of the chakra constructs one by one. Whenever one would move in to attack, he would easily maneuver around the clumsy strike, giving the clone a sharp rap on the head with his book to destroy it. One clone came at him with his arm reared back for a haymaker, but when Kakashi turned his back after dispersing it, he was suddenly tackled to the ground. It appeared that the real Naruto had been amongst the fray as well.

Sadly for the boy, Kakashi had already replaced himself with one of Naruto's own clones before the blonde ensnared him. The jounin reappeared on a nearby branch looking down upon the skirmish. Below him, Sasuke and Sakura were l in wait for the opportune moment to strike.

"You know, it's not nice to make your teammate do all the work." Kakashi said in his indifferent drawl. The two genin paled at his voice, and Sasuke quickly turned and threw a handful of shuriken at the teacher. Kakashi calmly lessened the flow of chakra to his feet and fell backwards to avoid the deadly stars. The boy and girl were surprised to see their teacher now hanging effortlessly upside down from the bottom of the tree limb. A loud crashing from the undergrowth signaled that Naruto had arrived on scene.

"You're not getting away this time, Sensei. Shadow Clone Jutsu!" Instantly, the whole area around the base of the tree was filled with a sea of orange-clad blondes. Kakashi had to quirk an impressed eyebrow at the feat but did not have long to contemplate it, for the next second he was fending of a huge en masse attack. As one, the clones charged the tree, scrambling to get up to him.

Normally, Kakashi would have just escaped to another nearby canopy, but he decided to humor the young genin and stand his ground. The jounin settled into one of his preferred taijutsu stances and began to beat back the waves of attackers. Every punch and kick thrown was fended of with only partial effort, and one after another the clones were dispelled, all while Kakashi remained hanging on the underside of his branch.

One of the Naruto's pulled out a pair of kunai in frustration. He lunged at Kakashi, making broad, sweeping swings with the knives. The sloppiness of the attacks allowed the jounin to dodge them with little difficulty, and when the one of Naruto's slashes left his guard wide open, his teacher countered. Kakashi grabbed Naruto by the wrists, twisting them slightly so that he was forced to drop the blades. He then gave the boy a light kick to the solar plexus.

Naruto was sent tumbling away until he came to a stop next to a nearby tree. The jounin was not yet finished, though, as he plucked the boy's own kunai out of the air and sent them sailing after him. The blond had just managed to stand up when the kunai hit him. They cut through the sleeves of his orange jumpsuit and pinned his arms to the tree trunk. Kakashi had to smile at his handiwork; while the knives would not hold Naruto for long, it would put him out of commission long enough for him to deal with the rest of the clones the boy had made.

It was then that the man saw two darker figures weaving their way through the throng of orange. Kakashi had grabbed one kage bunshin by the collar and dispersed it when he had to abruptly contort his head out of the way of the razor sharp kunai that had suddenly appeared from the smoke. He was able to catch a glimpse of red and pink in the direction the kunai had come from before his attention was brought back closer to home.

While Kakashi had been dodging ninja tool, Sasuke reached the base of the tree and used the numerous Naruto clones as jumping points to quickly ascend up to the jounin's level. The Uchiha extended his left leg out into a round house kick with the intent of nailing his sensei square in the back while his focus was elsewhere, but the jounin was still able to turn his torso around enough to block the shin with his left forearm. Sasuke then hooked the top of his foot on the bent elbow which allowed him to swing his body around the jounin's back towards the now unprotected bells.

Kakashi realized this and shot his own footout behind him at the genin. Sasuke was forced to twist his body out of the way, foiling his attempt, but the Uchiha was not finished, instead implementing his contingency plan. He pulled back the arm he had extended out towards the bell and snapped the other one forward, releasing the shuriken hidden in its grasp. The spinning blade cut through the air, easily severing the string tying the bells to the jounin.

Kakashi was the first to react, immediately severing his chakra connection to the tree branch. Sasuke was still trying to recover from his midair maneuver and would not be able to land in time to make another attempt for the freed bells. Sakura was a null factor, for her support position near the edge of the kage bunshin mass meant she would have to fight through the throng to even get close to the chimes, and the real Naruto had only now managed to free himself from where Kakashi had pinned him.

The jounin took all of this in as he dropped down. Below him, every Shadow Clone in the area was scrambling towards the falling chimes, desperate to reach them before their brief existences were ended. One made a heroic dive forward to grab the bells, and even managed to get ahold of them before Kakashi planted his feet on the clones back. However, this time it was the teacher that was tricked.

Kakashi's expert eye saw the slight wavering of the clone's outline right before he landed, but it was to late to divert his fall. Instead of landing on a shadow clone and dispersing it, the real Naruto substituted with the clone and toke the blow himself. The bunshin with the bells was now where the real one had been and proceeded to hightail it as fast and as far away as possible.

Underneath the jounin, Naruto grunted out in pain. Kakashi swiftly stepped off of his student, allowing two nearby clones to drag the blond away. Sasuke and Sakura saw this and followed along while the remaining Shadow Clones launched a final assault to prevent Kakashi from pursuing them. One by one, they disappeared, and whether by design or happy accident, the smoke of their dispelling only helped to further conceal the genin's retreat.

Once every clone was gone, Kakashi took a moment to ponder. For the first time since he had started taking on teams, a squad had managed to get the bells from him, and based on what he had scene during the exam the had also passed the second portion. Now, all that was left was to see what they did now that the test was over. Naruto had already shown he was willing to take a hit for the sake of the mission, but would he be willing to sabotage his own career for the sake of his teammates? Would they be do the same for him? There was one way to find out.

III

Kakashi swiftly found his students near the western edge of the training ground. All three were sitting on the ground panting in exhaustion, though both Sasuke and Naruto were trying to hide their tiredness. The blond of the group still held the bells clenched tightly in his hand. The jounin found a comfortable spot on a thick limb and waited to see what happened. He did not have to wait long.

"Heh, what's the matter Sasuke? That little run tire you out?" Naruto said, trying to goad the Uchiha. Sasuke simply ignored the mocking question, but Kakashi noticed that he tried to school his expression even more.

"Shut up, Naruto! Sasuke's probably just acting so that we don't feel bad for slowing him down. He probably could have gotten those bells all by himself." Sakura shouted, but she did have to admit they all looked worse for wear. It was strange; she felt more tired now than almost any other time she could remember. Naruto and Sasuke did not look much better. Her chastisement halted any further teasing, and the forest went silent, save for the soft wind rustling through the branches.

"So...what do we do now?" Naruto finally asked. Sakura bit the tip of her thumb out of nervous habit while Sasuke only grunted.

"I'm not going back to the Academy." The Uchiha finally stated after a few minutes, his tone adamant. Naruto whipped his head around to glare at the other boy.

"I'm not either; I barely made it out this time."

"Then you need more schooling, idiot." Sasuke said without turning to meet Naruto's gaze. The blond growled, but Sakura spoke up before he could say anything in response.

"Umm, Sasuke, Naruto, there's something else we have to think about."

"What's that Sakura?" Naruto questioned.

"Well, whoever gets a bell will become a full-fledged shinobi, so they will probably be busy doing missions a lot of the time. That means whoever doesn't will have more free time." The two only stared at her blankly, not understanding the point she was trying to make. "Whoever goes back to the academy can go visit Mewtwo-sensei sooner and more often."

The eyes of both boys widened dramatically at what she said. Ever since the three had left the hidden vault, they had all missed their newly found companions, even if one of them would deny it. The worst part was that they could not even sense them through their bond. Mewtwo had warned them that such a thing would happen and that such a thing was natural when partners were separated, but it did not help. It was somewhat maddening, like one of their limbs had gone numb overnight. They knew it was there, but they just could not feel anything.

Sakura's revelation left the genin in silent deliberation for even longer before. All three were trying to decide which was more important, their career as shinobi or reuniting with their friends. In the end, each one reached the same conclusion though none were willing to say it. Eventually, Naruto broke the silence.

"I think Sakura should get to go back. I mean, you were the top ranking kunoichi at the Academy, so you'll get to spend more time with Mewtwo-sensei than I would." His kind words shocked Sakura. "Besides, you're a lot better at using this Power thing than either of us. You would get more out of it than us." Sakura was almost tempted to accept Naruto's generous offer. She really wanted to see Chikorita again, but that would not be fair to Naruto and Sasuke.

"No way, Sasuke should go back. He's way more talented than I am." The fact that she could use this situation to compliment her crush was an added bonus. "My parents are watching me like hawks anyway. I will probably be able to slip away easier if I take a bell."

With both of their opinions voiced, Naruto and Sakura looked at Sasuke for his. His pale hands were folded in front of his face as he contemplated everything that had just been said. His thoughts inevitably turned back to his brother. Every moment of that night flashed through his mind's eye, and he knew what he had to do.

"Naruto, go back to the Academy." The blond's jaw almost dropped. He never thought he would hear the Uchiha say such a thing. "Face it, loser, you need all the help you can get." Well, the sentiment had been nice while it lasted, Naruto thought.

From within his leafy vantage, Kakashi listened to the entire debate, and two things immediately popped out to him. The first was that the three seemed oddly attached to this "Mewtwo-sensei". The jounin had never heard someone by that name, but then again, he was not that familiar with the Academy staff these days. He did make a mental note to check up on it later though.

The second thing he noticed was their tones. It was almost as if they all _wanted _to go back to the Academy. All he could do was shake his head and reveal the truth to them. They had passed the final test after all, no matter how strangely. The masked man dropped down to the ground and waved a hand at his students.

"Yo." The genin scrambled to their feet at his appearance, readying themselves as best they could. Kakashi noticed how ragged each of them seemed. Disfunctional personalities, the want to fail and go back for further schooling, and apparently extremely low stamina: he certainly had his work cut out for him, the Hatake thought.

"Seeing as how the timer has yet to go off, I could take those bells back from you," Kakashi said while getting to his feet. "But that would take away from my reading time. I guess I'll just pass you all instead."

Kakashi let out an audible chuckle at seeing his students falter. He certainly knew how to pull a fast one. All laughter quickly died in his throat, however. While he was mentally congratulating himself, Naruto, Sasuke, and Sakura collapsed to the ground.

The children's bodies began jerking around in short, violent spasms, their eyes rolled back in their heads. Limbs thrashed about wildly. Clear, runny vomit was choked up from their mouths as their stomachs tried to force every last drop of liquid. The acidic stench of bile clogged the air as any remnants of color was drained from their faces.

In the blink of an eye, Kakashi was moving. His fastest ninken, Ūhei, was already running as fast as possible to the nearest hospital by the time the dog's master had created five shadow clone. As gently as possible, the six jounin used their vastly superior strength to restrain the young ones' arms and legs. The clones near the kids' used their knees for this, so their hands were free to hold shaking children's heads to the side.

Fear gripped the very core of Kakashi's heart in a tight fist as he pressed Naruto's ankles firmly against the earth. A week ago, it had been his own failings that caused these children to suffer. This time was different. A week ago, he had been helpless. This time he was here.

He could not lose them again.


	5. Consequences Part II

**You know, I was going to have a very witty and pretty funny Christmas song parody for my disclaimer this chapter, but then my computer's power decided to crap out on me for over a month. As such, I figured the previous disclaimer would not be as fitting anymore and decided to go with this generic one instead. I should probably get to that now.**

**Meh, I'll do it eventually.**

III

_Awaken._

Naruto stirred as his mind slowly returned to the realm of consciousness. The first thing he noticed was the comfortable bed he was lying on, covered by soft, warm sheets. He almost let out a content sigh, but his brain decided at that moment to register the dull throbbing within his head. The blond reluctantly removed his hands from underneath the bedding to massage his temples. As the pain lessened, Naruto began to piece together what exactly had put him in such a state.

The last thing the boy could remember was Kakashi-sensei telling his team that they had managed to pass his test and become full-fledged genin. Naruto had barely started to celebrate when he felt a wave of exhaustion wash over his body, joined shortly by a crippling pain. Just thinking about the intensity of it was enough to make him shudder. Luckily for him though, he had blacked out shortly after it started.

Turning his focus back on the test itself, Naruto felt a smug smile form on his face. They may have only been able to spend a few days training with Mewtwo-sensei, but the impact was noticeable. Compared to trying to land a decent blow on the psychic Pokémon, stealing a bell away from Kakashi-sensei was a piece of cake. Mewtwo-sensei would spend hours sparring with the new trainers and not get a single scratch on him.

Any further contemplation on Naruto's part was halted when something fairly heavy suddenly landed square on his chest. The blond's eyes snapped open, and he sat straight up in the bed. Whatever the thing was tumbled down his torso to the foot of his bed. He blinked rapidly as his eyes grew accustomed to the dimly lit surroundings. Once he was able to see properly, Naruto looked down to discover Mudkip clamberingback onto his four stubby legs.

Joy filled the Uzumaki at the sight of his partner Pokémon. He immediately reached out to give the mud fish a welcominghug, but the water-type had other plans. Apparently, he did not enjoy being launched from his trainer's chest in such a manner, so when Naruto extended his arms, Mudkip slammed his forehead into the genin's nose. Mudkip grinned at the soft curses he heard his partner mutter. Naruto was about to retaliate when a jarring thought occurred to him.

"Wait a second; what the hell are you doing here, Mudkip? You're not supposed to be seen!" The blond said as he frantically tried to cover the Pokémon up with his bed covers. Mudkip, meanwhile, gleefully resisted his master's efforts, enjoying Naruto's rising frustration.

_'He is here because my hypothesis was correct.' _Naruto recognized the voice in his head and stopped his failing attempts to hide his Pokémon. His head whipped around as he tried to find the source. While doing so, he finally noticed that he was in a small, four bed hospital room. Propped up against her own headboard next to him was Sakura with Chikorita sitting calmly on her lap. Sasuke occupied the one diagonally across from the Uzumaki, and he could see an orange tail hanging out over the front side. Lastly, on the left side of the room from Naruto, Mewtwo floated serenely in the air by an open window, his face half illuminated by the light from Charmander's flame and the full moon outside.

"What hypothesis?" Sasuke questioned, leaning forward and cupping his hands in front of his face. Mewtwo closed his eyes for a moment before answering.

_'Seven days ago, the three of you drew upon the Power of Dominance in order to defend yourselves from my psychic attack. That same power is now causing your bodies to deteriorate.' _All three children stunned as the harsh reality Mewtwo's words sank in.

"But, you said people used this power long ago. Did this happen to them too?" Sakura said quietly, fear creeping into her voice. Mewtwo shook his head.

_'No. The human body became more accustomed to the strain the Power of Dominance placed upon it as the bond between our two species grew. When Pokémon disappeared, your kind's ability to use the power went as well. Centuries have passed since then, and it has now become completely dormant. Your bodies' deterioration is a sign of how weak that connection has become.' _Sasuke's hands tightened.

"You knew that this would happen and didn't tell us?" Mewtwo paused.

_'I had suspicions and theories, but there was only one way to be sure. Unfortunately, they proved to be more accurate than I had predicted. I did not believe the rate of deterioration would be as fast or the side effects as strong as they were. That, coupled with the exhaustion from your chosen career path, caused you to be in far greater peril than I intended, and for that, I must apologize.' _The room was silent.

"Well," Naruto started slowly. "It's not like you were trying to kill us."

"That still doesn't explain why didn't you tell us what was going on." Sasuke said accusingly.

_'Had I told you, you would have resisted the effects, even if it was only on a subconscious level. Any results gathered would have been inaccurate and dangerous to use as a basis.'_

"So, what do we do now?" Sakura asked.

_'From now on, your Pokémon shall remain with you. This should cause the Power of Dominance to stabilize across the bond you share just as it did the first time the three of you called upon it. You must take care to never be separated from them for long periods of time, or you will be faced with similar consequences.'_

"Wait, I thought you wanted Pokémon to remain a secret?" Naruto asked, puzzled.

_'Any secret, no matter how well kept, will eventually be revealed. The moment you three stumbled upon the vault, it was simply a matter of time until our existence was discovered. However, while we may not be able conceal ourselves for forever, we can control who learns of us first. As such, the best place to begin would be with your Third Hokage.'_

"Alright then, let's go find the Old Man!" Naruto shouted, swinging his feet over the side of his bed. Suddenly, the door to their hospital room swung open and in walked the God of Shinobi himself.

_'That will not be necessary, Naruto. He is already here.'_

III

Hiruzen Sarutobi sighed as he walked down the hallway of Konoha State Hospital. In his hands, he toyed with his favorite wooden pipe that he could normally be found smoking. Every Konoha hospital had a mandatory no smoking policy, so no matter how much the elder shinobi wished for its soothing fumes after the events of the past week, he would have to make do without.

Team Seven's disappearance had left a wake of unrest in its path. An entire subdivision of the ANBU was reassigned once more to scour the Hidden Leaf for any other hideouts Sarutobi's fallen student might have tucked away. Refunds had to be issued to clients of several time sensitive missions due to the assigned ninja having been pulled away to help in the search. News of the commotion was starting to trickle into other shinobi villages, and, to top it all off, there had been a confirmed sighting of Itachi Uchiha not twenty miles from Konoha.

The Third Hokage took off his hat and ran a hand through what little hair he had left. Despite how much everyone wished for the contrary, something in Hiruzen's bones told him that this was only the beginning. He sighed once more and continued on towards the final destination of his visit. It was all he could do for the time being.

While he walked, Sarutobi could not help but wonder why he had put off this particular room for so long. It was only his duties as Hokage that kept him from spending the entire day at their sides just like he knew Kakashi had. In fact, he had to order the jounin to go home and get some rest otherwise the man would have stayed up all night watching over them. Now he almost wished he had not done so, for the man had become a valuable confidant to Sarutobi over the years. Perhaps he might have been able to explain the tiny voice in the back of his head telling him to stay away from Naruto, Sasuke, and Sakura's room.

The Third Hokage turned the corner into the hall where the children were being kept and instantly knew something was wrong. The first thing that drew his attention was dim light emanating from their room. Every hospital in Konoha had a lights-out policy at night in order to conserve more power for critical areas such as the Intensive Care Unit. This could of course be waved in case of an emergency in less important wing, but Sarutobi neither saw nor heard anything that would indicate such an instance.

Of course, it could have been explained away as one the genin having simply turned on a light for one reason or another were not for the nature of the glow. Instead of the steady illumination of a bulb, this light danced and flickered like that of a small flame. That still left to many other viable explanations, so Sarutobi moved stealthily towards the room's entrance to gather more information on what was going on.

The hair on the back of Hiruzen's neck rose up during his silent approach. He felt as if there was some being observing him from just outside his field of vision, examining his every action, and it drew ever stronger as he closed in on the hospital room. Pushing it aside as best he could, the elder man quickly the concealment jutsu Jiraiya had taught him and peered through the wired window just in time to hear Naruto's voice cry out.

There in the room with the members of Team Seven were four bizarre creatures he had never seen before. The largest of them was floating roughly two feet in the air and appeared to be some sort of purple, humanoid cat. The other three were with the children in their beds who seemed to be taking the sight of them quite well. In fact, he would say they were happy to see them; Naruto and his were even playing together. He also noticed that the light was emanating from a flame burning on the tail of the one with Sasuke. The scene was so strange that the old man flared his chakra to make sure he had not been caught in an enemy's genjutsu.

It was then that the three children turned and looked at the larger monster. They then began talking to cat, and it was somehow communicating back. The creature never made a single sound or gesture, yet the genin were able to carry on a conversation with it. That did not mean he learned nothing from his observation. In fact, he picked up on a few very interesting bits of information, such as that the creatures were called Pokemon and were responsible for Team Seven's most recent trip to the hospital.

When Naruto suddenly shouted out, Sarutobi decided to reveal himself. At that same moment, the feeling in his mind solidified into a solid presence. It brushed across his consciousness, trying to make contact with him mentally. The elderly man immediately shut out every thought, preventing the probing specter from gaining any sort of foothold. It briefly poked at his mental walls before retreating back slightly. Once his inner defenses were secure, Hiruzen dispelled the camouflage jutsu and marched into the room.

"Oh, hey, Old Man. We were just about to go and find you."

"So I heard, Naruto." Sarutobi responded to the blond. The entire time, his gaze did not leave the humanoid monster in front of him. "I believe it is fair to assume that you are capable of both comprehending and communicating with me in some fashion." Mewtwo nodded calmly in response.

"Then I must ask that you come with me to be detained and questioned." Sakura fidgeted uneasily in her bed.

"Umm, Mewtwo-sensei says he can't do that." The God of Shinobi's eyes hardened.

"I'm afraid you do not have a choice." He said while beginning to gather up his chakra. Naruto waved his arms frantically.

"Whoa, hold on, Old Man! We can explain-"

"Silence, Naruto!" Sarutobi snapped. "The three of you vanished for four days. During that time, you came into contact with this thing within one of Orochimaru's abandoned facilities. That short amount exposure ended with you utterly debilitated and near comatose. That is not to mention the fact that this creature seems to have at least partial telepathic powers allowing it to influence if not simply control all three of you. I understand the situation well enough." Naruto wilted under the Third Hokage's admonishment.

"I will only ask once more. Surrender yourself peacefully or I will be required to use force." The creature did not respond. A minute passed, and it still showed no signs of cooperating. "Very well."

Hiruzen rapidly ran through a series of hand signs. Before he could finish the sequence, however, the creature lashed out with a tremendous mental assault. Sarutobi was rooted in place from the amount of concentration it took to hold back the overwhelming force. The psychological attack washed over his mind like water over a rounded river rock.

The God of Shinobi held strong forcing the monster into a stalemate. Should the latter's onslaught lessen, he would be able to perform the final seal of his jutsu, and if his will were to flag even the slightest, the creature would surely find a foothold and gain total access to his consciousness.

Around the two combatants, Naruto, Sasuke, Sakura and their Pokémon were visibly shaken by the battle. While the fight itself was impossible to see, the sheer, unbridled power exuding from both Mewtwo and the Third Hokage was slowly crushing them. The air was thick with energy.

The deadlock was finally broken when the tiles beneath Sarutobi's feet gained a slight blue outline before being ripped out from underneath him. Surprised by his sudden loss of footing, the man fell to one knee performing a dragon seal while Mewtwo's consciousness broke through his defenses.

"Lightning Style: Thunder Binding Jutsu!" Hiruzen slammed his palms against the hospital floor and electricity streamed forth from his hands. The bolts of energy ran up both of Sasuke's and one of Sakura's metal bed posts and used them as conductors to form a three sided barrier around the psychic Pokémon. The technique cost the Third Hokage dearly though, for Mewtwo used his psychic dominance to freeze the man in place. Sarutobi's body refused to respond to any commands from his brain.

'_Enough! I do not wish for any blood to be spilt tonight.'_ A strong, deep voice echoed through the old man's head. Sarutobi's eyes bore into the cat creature as it spoke to him. _'There is much we __must discuss and little time to do so. I intended to release my hold on you, but you must first __promise to not shut me out and listen to what I have to say. If not, you shall remain subjugated, and I will still say my piece. I will even remain within this cage you have generated should that ease you.'_

Sarutobi weighed his options. Someone else was sure to have felt what had just happened and raised an alert. He would not be surprised if there was a squad of ANBU already on the way here. However, he did not know how much the creature had to say. His best bet would be to acquiesce and stall for time. That, of course, would be pointless in this situation though because the monster was currently listening to his every thought. In the end, Hiruzen made his decision and could only hope it did not come back to haunt him.

III

Naruto, Sasuke, and Sakura sat in their beds, silently recovering from the war of wills they had just bore witness to. Between them, Pokémon and shinobi talked at length about many topics. Mewtwo explained to the Hokage the history of Pokémon and the origin of the Power of Dominance. The psychic-type also informed him about what had really happened when Team Seven disappeared. While they conversed, Sarutobi had sat down in a nearby chair and lit his pipe. He needed the nicotine to help him process everything he was being told, hospital rules be damned.

The elderly man leaned back in his seat and breathed out a billow of smoke from his nostrils once the two were done talking. Four ANBU had indeed shown up but were ordered to stand down by a motion from Sarutobi. Despite how outlandish what he was being told seemed, it was still the most plausible explanation for everything that had occurred in the past week.

Orochimaru's desire had always been immortality; the abominations he created were always a side effect of that endeavor. The creation of entirely new species made very little sense in that light, especially with the limited time and resources he had. That same reasoning ruled out the involvement of another shinobi village as there were simply far better and more efficient ways to spy on one another. If it were some other third party, why conduct such an elaborate rouse and then saddle their creations to three newly graduated genin? He was starting to believe Mewtwo, though he did require more proof.

"You mentioned your vault was hidden within the village. Would you allow a team chosen by me to examine its contents and records?"

'_Three people at maximum, and they can only do so under my watch. They are not allowed to remove any of the vaults contents. I will only provide sufficient records to prove the validity of my story.'_

"Agreed." Sarutobi said, making a note to have Inoichi Yamanaka personally head the team. The room was quiet for several minutes after that while the Hokage thought about the situation. He let out low, thoughtful hum before speaking again. "In the morning, I shall begin the process of designating Pokémon as a new type of summons. This will allow me to severely punish any who try to tamper with anything related to your species without your consent. It will also allow you to have access to certain village resources. I can have one of the children deliver the specifics to you to look over before I finalize it."

'_It is acceptable.' _Mewtwo answered. Sarutobi stood up and cracked his back. The electric barrier that had surrounded the legendary disappeared while he turned towards the door. Looking back over his shoulder, he addressed the children that had been watching the proceedings

"I suggest the three of you get some rest as you can. Tomorrow will be a busy day for all of us."

III

**IIIII LIIIIIIIIIIIIVVVEEE! **

**Holy crap, does the universe have some kind of rule against me updating my stories in less than two months? Seriously, I was on track to get this to you guys almost a month ago, and then my laptops power button decided to stop working. I don't care if computer troubles is a cliché excuse; do you know how frustrating it is to know your computer is perfectly capable of running, but you just can't turn the damn thing on? AAAAAAAAGGHHHH!**

**Phew, now that I got that of my chest, I really do apologize for always being so late with this story. I swear baby, I can change. Just give me once chance. **

**Also, the reference was from Castlevania. More specifically, it is the phrase "Power of Dominance" which in that series is how Dracula, Alucard, and Soma are able to control the souls of monsters. No, that does not mean this will be a crossover with those games as well, I just needed a name for the power in my story, so I co-opted the phrase since it seemed to fit rather well with my mythos. **

**See you all next time. This is Glock3bb signing out.**


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